Code Breaker
by Opheaphea
Summary: Clary is a 25 year old cryptanalyst working for the FBI. Jace is the Bureau's best field agent, hell-bent on catching the city's most notorious murderer. When Clary's skills are needed for Jace's biggest case yet, they find themselves falling deeper into a world of crime where nothing is as it seems, and being in each other's lives is only going to complicate things more... AU/AH
1. Prologue

**Summary:** Clary Morgenstern is a 25 year old cryptographer for the FBI in New York. Jace Herondale is the Bureau's best field agent, hell-bent on catching the city's most notorious murderer. When Clary's skills are needed for Jace's biggest case yet, they find themselves falling deeper into a world of crime where nothing is as it seems, and being in each other's lives is only going to complicate things more…

 **Disclaimer: I do not, unfortunately, own The Mortal Instruments or any of it's characters.**

* * *

 **Prologue – Part 1**

He knew it was coming. They had been building up to this for a while. He would have done the same thing in her situation, no doubt about it. But he wasn't. In her situation, that is. So just because he knew it was the best thing for everyone, including him, it didn't mean he liked it, it didn't mean he was okay with it, and it _certainly_ didn't mean he was going to put up with it. At least, not without a fight.

So whilst Jace Herondale wasn't surprised about what was coming to him - in fact, he was even prepared for his mother's betrayal - he still felt that his sudden, child-like outburst was warranted, given the situation.

"What the hell?! You can't do this!" Jace exclaimed, jumping out of the plush chair that faced one of the most foreboding characters he had ever met; his mother.

Maryse Lightwood sat behind a mahogany desk on the top floor of the FBI headquarters in Manhattan, New York. The light shining in through the glass wall behind accentuated not only her sharp features, but Jace's sheer terror at defying her. Usually, she was remarkably good natured, despite the infamous reputation she had acquired as she had worked her way up through the ranks at the Bureau. However, it was at times like this when Jace remembered exactly how his adoptive mother had become the Director of America's biggest defense against crime, and it wasn't because of her kind-hearted nature.

"Jace," she chastised, letting out a sigh as she rubbed her temples, trying to prevent the oncoming headache. "This is for your own good. You and your brother can't carry on like this. You both knew it was only a matter of time before someone stepped in and you and Alec had to accept help."

"But this is our case! We're the best agents the Bureau has, and you know it. We can do this on our own."

"The best _field_ agents, maybe, but certainly not the best in _every_ department. You could do with some real help, Jace, especially considering the only leads you've ever had are all in a code that you two could barely decipher on your own, and that's assuming you even got it right!"

"Just give us a little longer..."

"You've been chasing this guy for 2 years –"

"But he only resurfaced a week ago! We've got a lead. Maryse, please." Jace softened his golden eyes and lowered his head, looking at his adoptive mother from under his lashes.

"That face hasn't worked on me since you were ten." Maryse glared at his attempt at a puppy face, and he rearranged his features to reciprocate the gesture.

"Besides, you and Alec were foolish to think you could take on this case with no aid whatsoever. We're talking about one of the most notorious serial killers we've had in _decades_. Unless you let more agents onto this case, innocent people will die, and for what? the price of your fragile ego? That is _not_ a sacrifice I am willing to make." Maryse knew Jace would respond to that – despite what he would have others believe, he wasn't as heartless as he let on.

"How many others?" Jace admitted defeat and sank back down into the grey leather chair in front of Maryse, head in his hands.

"Two more field agents; Isabelle, of course, and Magnus Bane, whom I believe you know. I'm assigning you a new forensic analyst, Malcolm Fade, and from the Cybercrime Division, Simon Lewis and Clarissa Morgenstern."

"Why do we need people from Cybercrime?"

"Your new lead – it's the encrypted memory stick, right?"

"How did you…?" Jace trailed off, shaking his head. Maryse was the Director. She knew everything that went on in this place - nothing got past her.

"Simon's the tech guy," She explained. "He'll help you with the memory stick and any other technical problems you may run into."

"And the Morgenstern girl?" Jace enquired.

"She's the FBI's best cryptanalyst. Your guy seems to have a thing for leaving codes and ciphers behind. Clarissa can deal with that."

"Do we really need this many people? Alec and I are so close!" Jace pleaded in a last ditch effort he knew wouldn't work.

"And you would be even closer if you had enlisted help before!" Maryse sighed, exasperated at her son's stubbornness.

Jace took a deep breath, standing up to leave.

"Anything else, Director?"

"Come on Jace, don't use that title with me, I'm your mother for goodness sakes. And you're still leading the investigation – You'll be calling all the shots." Jace let out an inaudible breath as some of the tension was released from his shoulders. _At least there was that_ , he thought as he started to leave.

"Oh, and Jace?" Maryse called out after him, his hand hovering over the doorknob, desperate to escape.

"Yes?" His strained voice managed to reply.

"Try not to screw this up."

* * *

 **Prologue - Part 2**

Clary sighed heavily as she tried to fax over the paperwork for one of her more recent cases. She would have thought that for a cybercrime division they would have a more advanced system in place, but alas, her various complaints to the Head of Department had gone unnoticed. So here she was, wrestling with a machine built in the 1800's that was going to permanently damage her hand if it didn't start to respond to her brutal beatings.

After almost two years in the Bureau – having spent one of them in the Cybercrime Department – the workload was beginning to catch up with her. Of course, if she'd spent less time playing Assassin's Creed with Simon and Maia and more time doing what she was supposed to, maybe she wouldn't be having this problem.

"Ouch! What was that for?" Clary cried out indignantly. She reached up to soothe the back of her head, which had just been brutally assaulted by the file Simon was holding.

"C'mon, sleepyhead, the Director has requested our presence." Simon said, not waiting for Clary to catch up before moving on without her.

"I'm not sleepy, I'm just…"

"Clary, you've yawned ten times in the last three minutes and have ink all over your face from where you fell asleep on your hand, despite the three cups of coffee at your desk from the last hour alone." Simon's patronizing glare would have been justified, had he and his Xbox not have been the reason she was so tired.

Clary looked at her reflection in one of the many floor to ceiling windows in the building. She did, in fact, have blue ink smudged across her right cheekbone.

"So why does Mrs Lightwood want to meet with us?" Clary asked as she tried to conspicuously rub off the ink on her face.

"No idea." A quick look in the nearest reflective surface - the elevator doors they were standing in front of - told her she was doing more harm than good to her face. The doors opened and Simon pressed the button for the top floor.

A minute or two later, she and Simon were walking down the corridor on the top floor in silence, too nervous to say anything. The Director of the largest FBI headquarters in the country didn't concern herself with trivial matters. A million ideas of why the Director had requested to meet with them ran through Clary's mind. None of them were good.

When they finally made it to Maryse Lightwood's office, Clary was visibly shaking; she probably should have laid off the coffee. Simon opened the door. In front of them was the probably one of the most daunting images she had ever seen. Maryse sat at her elaborate desk, looking increasingly intimidating in her expensive designer suit, her dark hair pulled back tightly into a bun.

A handful of other agents were there, two of which she recognised as Maryse's kids - the resemblance was uncanny. The only other person she vaguely recalled was Malcolm, from forensics. She had worked a few cases with him a while ago, but they weren't really close. Among them was a man wearing what surmounted to about fifteen violations of the dress code and three colours she didn't know existed, and another sitting next to him whose head was just visible over the back of the armchair he sat in, with hair so blond it seemed to suck all other colours out of the room. Of course, that could have just been the Director's grey-on-grey colour scheme.

"Mr Lewis, Miss Morgenstern, how nice of you to join us." The Director addressed them in an icy voice. Clary's worst fears had been confirmed. "Please, take a seat." The Director gestured in front of her with one of her perfectly manicured hands, the other one of which was resting on top of the stack of files situated in front of her.

"I'm sure you're all wondering why I've called you here, and the answer is simple. You are all the best of the best in your chosen fields."

"Wait, so we're not getting fired?" Simon voiced Clary's suspicions, earning a glare from the Director for the interruption.

"That depends, Mr Lewis. Have you done anything for me to fire you for?" The Director raised an elegant eyebrow as Simon shrank into his seat and mumbled in denial. Clary guessed now probably wouldn't be the best time to mention Simon had inadvertently set the photocopier on fire last week. And it wasn't the first time it had happened this year. "You're not getting fired." Maryse clarified. "Quite the opposite, actually. I'm putting you all on the biggest murder case this city has ever seen."

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 **Hi there! This is my first ever fanfiction (sort of). The title is a work in progress, so for the few people amazing enough to read my work, just be aware that it might change in the near future. Also, I am aware that the chapter length for this one is a bit short, so just bare with me, because they will get longer! Any follows, favorites or reviews will be majorly appreciated. Kudos.**

 **~Opheaphea**


	2. Chapter One

**Warning: Contains depictions of violence and death that some people may find uncomfortable.**

 **Chapter One**

Clary stepped through the door Simon was holding open for her, grateful to be rid of the overpowering scent of lemongrass that seemed to have taken up residence in the Director's office. She waited next to Simon as he kept the door open for everyone, not missing the way his face flushed deep red when Isabelle threw a wink his way as she sauntered out of her mother's domain.

"So," Jace was the last one to step through the door, stopping in front of Simon. "I guess I'll have to hand this over." Jace reached into his pocket as he spoke, holding out a slim piece of metal in his left hand.

"Wait, you were carrying the only lead we have in your pocket? What happened to the evidence locker?" Simon raised an eyebrow, taking the memory stick from Jace's open palm.

" _My_ only lead." Jace emphasised. It was blatantly obvious that it wasn't his idea to let more people on this case. Clary may not have known who he was when she first laid eyes on him, but as soon as she had heard his name, things began to fall into place. Jace Herondale was practically a celebrity within the Bureau when it came to the number of cases he had closed, despite his siblings being the only people Jace would even consider working with - he was notoriously famous for refusing to work with other agents unless absolutely necessary, so for him to accept so much help from so many people, things must have been pretty bad. "And no, nothing happened to the evidence locker, unless you count it being monitored by a bunch of under-qualified children with no credentials who either don't know how to use a filing system, or are taking the weed we get from the drug busts to fuel their addiction since their parents cut them off. You heard what Maryse said; this is one of the biggest cases we've had in years. I'm not letting those morons over at evidence ruin this for me."

"Jace! You'll have to excuse him, he doesn't like sharing, especially when it involves his cases." Maryse's daughter and Jace's adoptive sister looked apologetically at Simon as she batted her lashes, which dimmed Simon's look of rage at Jace outburst somewhat. Not enough to stop him from picking a fight with him, though.

As Jace and Simon continued to bicker over the importance said morons in the Bureau's hierarchy, Clary relayed the meeting she just had, still trying to make sense of it all.

* * *

" _I'm putting you all on the biggest murder case this city has ever seen."_

The room fell into an uncomfortable silence whilst everyone digested those words. Malcolm was the first to raise his voice. "What exactly is this case about?" He tentatively asked.

"Women all around New York are disappearing without a trace, no leads whatsoever, and turning up a few days later." Maryse opened up the file on her desk and spread out small sheets of paper across it.

"Well, that doesn't seem so bad." Magnus said with obvious caution in his voice. There was more to it than that, and they all knew it.

"These are pictures of the bodies." Maryse said grimly. Clary looked down at the papers at the desk only to see the rather gruesome remains of the victims. She wished she hadn't.

"As you can see, they are all in similar states, but they didn't start out like this. They all looked completely different. None of them had anything in common with each other except for their post code – that is, until our guy got to them." Maryse pointed to different aspects of the pictures as she continued, Simon's face growing greener with each passing word.

"Their faces have been surgically altered to all look similar; see the scars around the ears and under the jaw. They've all been scalped, rather meticulously I might add, suggesting the perpetrator wanted to keep the scalp intact. Speaking of which, traces of ammonia has been found on the bodies, meaning all their hair was probably dyed. Their nails have been pulled out, fingerprints sanded off and skin bleached, making it rather hard to identify the bodies, or the perpetrator." Maryse finished with a look of disgust on her face, one Clary was pretty sure she, and everyone else in the room, wore too. Much to everyone's chagrin, Maryse continued.

"The bodies have been found in alleyways, in the middle of the street, all within a thirty mile radius from here."

Clary's eyes furrowed in confusion.

"That doesn't make any sense. Why would he go through all that trouble to make the bodies look the same, only to kill them and dump them in the middle of one of the busiest cities in the world, not even bothering to hide them properly or destroy them? His behaviour doesn't add up; why bleach their skin, but put the bodies in plain view of the general public? It suggests he both wants to get caught and doesn't at the same time. It's almost like he's -"

"-Like he's playing a game. One he has no intention of losing, and is probably rigged." The stranger sitting in the chair next to her spoke up for the first time since she'd arrived. Clary couldn't help but stare as she laid her eyes on him. There was something about him. Maybe it was that he had finished her sentence, had known her exact train of thought. Or maybe it was the way he seemed to command the room's attention with less than a sentence. Or it could have been the intense way he was staring at her, with those sun-like orbs he had for eyes and his halo of golden hair...

"Exactly." Maryse pulled Clary out of her artistic analysis of the man next to her, something she had a habit of doing now and again. Her cheeks flushed as she realised she had been staring way too long, as was evident in glare she received from the Director as she continued to speak.

"But he doesn't want to make it easy for us. As if your analysis wasn't proof enough, he seems to leave behind clues. cryptic messages that come along with the bodies; this is where you two come in." She gestured towards Clary and Simon. "Now, these clues have all been fairly simple in the past, but none of them have ever lead to anything substantial. Addresses that lead to the middle of nowhere, taunting slurs that mean next to nothing, that sort of thing. However, the culprit went MIA about six months ago. He resurfaced a few days back and he seems to have upped his game. He left an encrypted memory stick at the scene. That's for you, Simon. Now, we're guessing that whatever is on that file will be slightly harder to crack than the previous messages he's left behind, given that it's already much more advanced than anything he's sent our way before. Clary, that's where you come in. Whilst you're waiting for Simon to decrypt the file, I'll have the old clues sent over to you in case we missed anything the first time round, and once Simon's done, we can expect there to be another code for you to break on that file. The rest of you are here to help with the field work, and Malcolm, check if there's anything in these photos of the bodies that we've missed. Alec and Jace will be leading the investigation. You report to them from now on." Maryse gestured towards her son and the blond boy who had interrupted Clary.

"This goes without saying, but this case is your top priority from now on. It takes precedent over anything else you have going on. We've been at this for years and have absolutely nothing to show for it; the Board is getting impatient. You have three months."

* * *

"Clary?" Simon was waving his hand in front of Clary's face, breaking her out of her reverie.

"Yeah? sorry, Si. I'm just a bit out of it."

"Can't imagine why, after a meeting like that." Maryse's scantily clad daughter piped up. "Did she really have to show us those pictures? So morbid." The stunning Brunette introduced herself. "Isabelle Lightwood. Clarissa Morgenstern, right? It's great to finally meet you. I've heard a lot about your work, especially the stuff you did before you joined the Cybercrime Department. Why'd you defect from being a field agent?"

"Err, well- I…"Clary was saved from having to answer one of the Lightwood's questions by the other sibling.

"Izzy, stop being so nosey. I'm sorry, she's always like that I'm afraid. I haven't managed to find an off switch for her yet. I'm Alec, by the way. Izzy and Jace's brother." Clary couldn't have been more grateful towards the dark-haired, blue-eyed beauty for saving her from Isabelle's line of questioning.

"I'm Clary, from Cybercrime, as is my friend Simon here." Simon looked at her with gratefulness for doing the introductions on his behalf. He looked as if he was going to be sick if he even so much as opened his mouth to speak. Clary couldn't blame him after a meeting like that.

"Magnus Bane, at your service." The man wearing at least two different animal prints said with a flourish. "I don't believe I've had the pleasure of meeting most of you, but some of you lucky souls know me _all_ too well." Magnus said with a sly look directed towards Alec that Clary had a feeling she wasn't supposed to see.

"I'm Malcolm, not that I need introducing. I believe I've worked cases with all of you before at one point or another."

"Well, I don't think an introduction from me will be necessary, but I'll do it anyway, just because I know how much you all love to hear the sound of my voice." The Golden boy who had captured her gaze earlier spoke as he leaned nonchalantly against the wall. "I'm Jace, but you can all call me hot stuff if you prefer. And _you_ ," Jace placed a lazy wink in her direction. "Can call me anytime."

"So I was thinking," The Golden Boy moved on before Clary had time to react to what Jace was implying. "We should all go out tonight. Most of us have never worked together before, and we only have a few months to pull this off, so we should learn how everyone else works. You know, strengths, weaknesses, how much liquor you can take, that sort of thing.

"I dunno…" Simon said dubiously, biting his lower lip.

"It's all on me." Jace insisted.

"Well , I'm never one to pass up on a wild night out, especially when there's free booze involved. Tell me the when and where and I'll be there." Magnus agreed.

"Pandemonium. Tonight at eight."

"I guess..." Simon confirmed, and Clary and the others nodded in agreement.

"Great. Now, Clary, all the codes this guy has left behind are in evidence. We can go get them now if you want."

"Sounds great."

Everyone else dispersed, and Clary and Jace made their way down the corridor and into the lift, Jace pressing the button for the lowest floor.

"Er... Clary?" Jace started after the awkward silence became too much to bear.

"Yes?"

"You've got something on your cheek." Jace traced a delicate line across his own cheekbone with his fingertip, indicating to where Clary still had the remnants of ink from earlier.

"Oh, yeah - right." Clary blushed as she reached up to rub off the ink.

"What now?" Clary asked impatiently as Jace struggled to hold in his laughter.

"You're just making it worse. Here, let me." Jace took a step closer to her, reached up with his thumb and started to gently rub away at Clary's stained cheek, of which she was now sure was more red than blue from all the blood rushing to her face. He was so close she could smell his aftershave and note the different shades that made up his impossibly golden eyes. So close she could see the slight incisor in his front tooth as he bit his bottom lip in concentration. So close she could see the sharp angle of his cheekbones and the way his hair fell over his eyes so perfectly. So close, in fact, that is was a mystery to her as to why it took her so long to realise that Jace was staring back at her just as intensely as she was him, and that he had stopped working on the ink and yet still had his hand on her face. It was also a mystery as to why, after realising all of this, she still didn't step away from him like every part of her mind was telling her to, but instead leaned into the warmth of his hand. She may have been able to chalk up her staring to artistic curiosity, but that was something else entirely.

The bell for the lift rang as the doors slid slowly open, and just like that, the moment - or whatever the hell it was that had just happened - was over.

"Thanks." Clary said breathlessly as Jace lowered his hand. A quick look in the mirrors encasing the interior of the lift told Clary the smudge was gone. Her blush, however...

"Anytime." Jace replied, sounding a little too pleased for Clary's liking as they stepped out into the corridor and let the doors close behind them.

"So, where exactly is Pandemonium?" Clary asked as the silence stretching through the hall became too much.

"You've never been?" Jace's eyebrow shot up as Clary shook her head in the affirmative. "The field agents go all the time. I guess I just presumed it was where all the other departments went to let their hair down, too."

"I wouldn't know, even if it was. I'm more of a stay at home and watch Daredevil kind of person."

"What is it now?" Clary sighed as Jace pursed his lips at her comment.

"Nothing, I just didn't have you pegged as a Marvel's fan."

"What, you mean you've known me for all of half an hour and you _still_ don't know all my secrets? I'm shocked." Clary joked as she and Jace entered the musty evidence locker.

"Laugh all you want, Ginger, but I've got to say, I am just a little disappointed in you. I'd have thought that someone with capable of the excellent evaluating prowess you showed earlier would be able to tell that DC is _clearly_ the better choice." Jace lifted a box from one of the top shelves, flexing his barely concealed muscles under his t-shirt as he did so. He set the box down and opened it up. Scanning through, he took out a thin file and handed it Clary, their hands brushing slightly as he did so.

"Ok, I'm going to let that one slide, but you better hope I'm not holding anything heavy the next time you make a comment like that."

"Like you could take me, Morgenstern." Jace shook his head in amusement, and Clary blushed at the double entendre. What was wrong with her today? "Anyway, I'll text you the address for Pandemonium. Be there on time. Izzy has a remarkably short attention span, so if she's kept waiting too long, she'll disappear into the crowds and we won't see her for the rest of the night."

"Got it. Simon and I will be there by midnight, one o'clock at the latest." Clary teased as she stepped into the hallway and made her way back to her desk, unaware of what was coming her way.

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 **I promised a longer chapter, so I hope you enjoyed! I'd just like to say a huge thank you to everyone who followed, favourited, reviewed, or even just checked out the first chapter. I would especially like to thank the guest reviewers, who I unfortunately could not reply to, but I'd still like you to know that you guys made my day! I just want to point out that this chapter was a one off in terms of the content; everything from here on out will be more focused on catching the guy, rather than the gruesome details of what he does to his victims, so don't worry if that stuff wasn't your cup of metaphorical tea. Till next time,**

 **~Opheaphea**


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